Make imports explicit, test with ExplicitImports.jl (#188)

* Fixes for ExplicitImports.jl * Add package tests * Add separate `test/linting.jl` file
adrhill · Sep 4, 2024 · 45be93b · 45be93b
1 parent 116f027
commit 45be93b
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diff --git a/ext/SparseConnectivityTracerDataInterpolationsExt.jl b/ext/SparseConnectivityTracerDataInterpolationsExt.jl
@@ -6,9 +6,8 @@ if isdefined(Base, :get_extension)
     using SparseConnectivityTracer: AbstractTracer, Dual, primal, tracer
     using SparseConnectivityTracer: GradientTracer, gradient_tracer_1_to_1
     using SparseConnectivityTracer: HessianTracer, hessian_tracer_1_to_1
-    using SparseConnectivityTracer: Fill # from FillArrays.jl
+    using FillArrays: Fill # from FillArrays.jl
     import DataInterpolations:
-        AbstractInterpolation,
         LinearInterpolation,
         QuadraticInterpolation,
         LagrangeInterpolation,
@@ -19,15 +18,14 @@ if isdefined(Base, :get_extension)
         BSplineInterpolation,
         BSplineApprox,
         CubicHermiteSpline,
-        PCHIPInterpolation,
+        # PCHIPInterpolation,
         QuinticHermiteSpline
 else
     using ..SparseConnectivityTracer: AbstractTracer, Dual, primal, tracer
     using ..SparseConnectivityTracer: GradientTracer, gradient_tracer_1_to_1
     using ..SparseConnectivityTracer: HessianTracer, hessian_tracer_1_to_1
-    using ..SparseConnectivityTracer: Fill # from FillArrays.jl
+    using ..FillArrays: Fill # from FillArrays.jl
     import ..DataInterpolations:
-        AbstractInterpolation,
         LinearInterpolation,
         QuadraticInterpolation,
         LagrangeInterpolation,
@@ -38,7 +36,7 @@ else
         BSplineInterpolation,
         BSplineApprox,
         CubicHermiteSpline,
-        PCHIPInterpolation,
+        # PCHIPInterpolation,
         QuinticHermiteSpline
 end
 

diff --git a/ext/SparseConnectivityTracerLogExpFunctionsExt.jl b/ext/SparseConnectivityTracerLogExpFunctionsExt.jl
@@ -2,10 +2,60 @@ module SparseConnectivityTracerLogExpFunctionsExt
 
 if isdefined(Base, :get_extension)
     import SparseConnectivityTracer as SCT
-    using LogExpFunctions
+    using LogExpFunctions:
+        LogExpFunctions,
+        cexpexp,
+        cloglog,
+        log1mexp,
+        log1mlogistic,
+        log1pexp,
+        log1pmx,
+        log1psq,
+        log2mexp,
+        logabssinh,
+        logaddexp,
+        logcosh,
+        logexpm1,
+        logistic,
+        logit,
+        logit1mexp,
+        logitexp,
+        loglogistic,
+        logmxp1,
+        logsubexp,
+        xexpx,
+        xexpy,
+        xlog1py,
+        xlogx,
+        xlogy
 else
     import ..SparseConnectivityTracer as SCT
-    using ..LogExpFunctions
+    using ..LogExpFunctions:
+        LogExpFunctions,
+        cexpexp,
+        cloglog,
+        log1mexp,
+        log1mlogistic,
+        log1pexp,
+        log1pmx,
+        log1psq,
+        log2mexp,
+        logabssinh,
+        logaddexp,
+        logcosh,
+        logexpm1,
+        logistic,
+        logit,
+        logit1mexp,
+        logitexp,
+        loglogistic,
+        logmxp1,
+        logsubexp,
+        xexpx,
+        xexpy,
+        xlog1py,
+        xlogx,
+        xlogy
 end
 
 ## 1-to-1 functions

diff --git a/ext/SparseConnectivityTracerNNlibExt.jl b/ext/SparseConnectivityTracerNNlibExt.jl
@@ -4,10 +4,58 @@ module SparseConnectivityTracerNNlibExt
 
 if isdefined(Base, :get_extension)
     import SparseConnectivityTracer as SCT
-    using NNlib
+    using NNlib:
+        NNlib,
+        celu,
+        elu,
+        gelu,
+        hardswish,
+        hardtanh,
+        hardσ,
+        leakyrelu,
+        lisht,
+        logcosh,
+        logσ,
+        mish,
+        relu,
+        relu6,
+        selu,
+        sigmoid_fast,
+        softplus,
+        softshrink,
+        softsign,
+        swish,
+        tanh_fast,
+        tanhshrink,
+        trelu,
+        σ
 else
     import ..SparseConnectivityTracer as SCT
-    using ..NNlib
+    using ..NNlib:
+        NNlib,
+        celu,
+        elu,
+        gelu,
+        hardswish,
+        hardtanh,
+        hardσ,
+        leakyrelu,
+        lisht,
+        logcosh,
+        logσ,
+        mish,
+        relu,
+        relu6,
+        selu,
+        sigmoid_fast,
+        softplus,
+        softshrink,
+        softsign,
+        swish,
+        tanh_fast,
+        tanhshrink,
+        trelu,
+        σ
 end
 
 ## 1-to-1

diff --git a/ext/SparseConnectivityTracerNaNMathExt.jl b/ext/SparseConnectivityTracerNaNMathExt.jl
@@ -2,10 +2,10 @@ module SparseConnectivityTracerNaNMathExt
 
 if isdefined(Base, :get_extension)
     import SparseConnectivityTracer as SCT
-    using NaNMath
+    using NaNMath: NaNMath
 else
     import ..SparseConnectivityTracer as SCT
-    using ..NaNMath
+    using ..NaNMath: NaNMath
 end
 
 ## 1-to-1

diff --git a/ext/SparseConnectivityTracerSpecialFunctionsExt.jl b/ext/SparseConnectivityTracerSpecialFunctionsExt.jl
@@ -2,10 +2,98 @@ module SparseConnectivityTracerSpecialFunctionsExt
 
 if isdefined(Base, :get_extension)
     import SparseConnectivityTracer as SCT
-    using SpecialFunctions
+    using SpecialFunctions:
+        SpecialFunctions,
+        airyai,
+        airyaiprime,
+        airyaiprimex,
+        airyaix,
+        airybi,
+        airybiprime,
+        airybiprimex,
+        airybix,
+        besseli,
+        besselix,
+        besselj,
+        besselj0,
+        besselj1,
+        besseljx,
+        besselk,
+        besselkx,
+        bessely,
+        bessely0,
+        bessely1,
+        besselyx,
+        beta,
+        cosint,
+        digamma,
+        ellipe,
+        ellipk,
+        erf,
+        erfc,
+        erfcinv,
+        erfcx,
+        erfinv,
+        expint,
+        expinti,
+        expintx,
+        gamma,
+        invdigamma,
+        jinc,
+        logbeta,
+        logerfc,
+        loggamma,
+        sinint,
+        sphericalbesselj,
+        sphericalbessely,
+        trigamma
 else
     import ..SparseConnectivityTracer as SCT
-    using ..SpecialFunctions
+    using ..SpecialFunctions:
+        SpecialFunctions,
+        airyai,
+        airyaiprime,
+        airyaiprimex,
+        airyaix,
+        airybi,
+        airybiprime,
+        airybiprimex,
+        airybix,
+        besseli,
+        besselix,
+        besselj,
+        besselj0,
+        besselj1,
+        besseljx,
+        besselk,
+        besselkx,
+        bessely,
+        bessely0,
+        bessely1,
+        besselyx,
+        beta,
+        cosint,
+        digamma,
+        ellipe,
+        ellipk,
+        erf,
+        erfc,
+        erfcinv,
+        erfcx,
+        erfinv,
+        expint,
+        expinti,
+        expintx,
+        gamma,
+        invdigamma,
+        jinc,
+        logbeta,
+        logerfc,
+        loggamma,
+        sinint,
+        sphericalbesselj,
+        sphericalbessely,
+        trigamma
 end
 
 #=

diff --git a/src/SparseConnectivityTracer.jl b/src/SparseConnectivityTracer.jl
@@ -9,7 +9,7 @@ using LinearAlgebra: LinearAlgebra, Symmetric
 using LinearAlgebra: Diagonal, diag, diagind
 using FillArrays: Fill
 
-using DocStringExtensions
+using DocStringExtensions: DocStringExtensions, TYPEDEF, TYPEDFIELDS
 
 if !isdefined(Base, :get_extension)
     using Requires

diff --git a/src/operators.jl b/src/operators.jl
@@ -223,7 +223,7 @@ for op in ops_2_to_1_fsc
 end
 
 # gradient of x/y: [1/y -x/y²]
-SparseConnectivityTracer.is_der1_arg2_zero_local(::typeof(/), x, y) = iszero(x)
+is_der1_arg2_zero_local(::typeof(/), x, y) = iszero(x)
 
 # ops_2_to_1_fsz: 
 # ∂f/∂x    != 0

diff --git a/src/overloads/arrays.jl b/src/overloads/arrays.jl
@@ -111,12 +111,12 @@ function LinearAlgebra.eigen(
 end
 
 ## Inverse
-function LinearAlgebra.inv(A::StridedMatrix{T}) where {T<:AbstractTracer}
+function Base.inv(A::StridedMatrix{T}) where {T<:AbstractTracer}
     LinearAlgebra.checksquare(A)
     t = second_order_or(A)
     return Fill(t, size(A)...)
 end
-function LinearAlgebra.inv(D::Diagonal{T}) where {T<:AbstractTracer}
+function Base.inv(D::Diagonal{T}) where {T<:AbstractTracer}
     ts_in = D.diag
     ts_out = similar(ts_in)
     for i in 1:length(ts_out)
@@ -132,7 +132,7 @@ function LinearAlgebra.pinv(
     t = second_order_or(A)
     return Fill(t, m, n)
 end
-LinearAlgebra.pinv(D::Diagonal{T}) where {T<:AbstractTracer} = LinearAlgebra.inv(D)
+LinearAlgebra.pinv(D::Diagonal{T}) where {T<:AbstractTracer} = inv(D)
 
 ## Division
 function LinearAlgebra.:\(
@@ -143,7 +143,7 @@ function LinearAlgebra.:\(
 end
 
 ## Exponential
-function LinearAlgebra.exp(A::AbstractMatrix{T}) where {T<:AbstractTracer}
+function Base.exp(A::AbstractMatrix{T}) where {T<:AbstractTracer}
     LinearAlgebra.checksquare(A)
     n = size(A, 1)
     t = second_order_or(A)

diff --git a/test/Project.toml b/test/Project.toml
@@ -8,6 +8,7 @@ ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"